I am sorry that you have been having problems - and hope that I can help.
I just tested FTP right now - and it is working for me. My guess is that
the server name being entered is incorrect. You want this to be
"usegalaxy.org" (not "use_*r*_galaxy.org") for the main public site (or
be whatever the base url is for the other public servers, that are
supporting FTP, you may be using). On any server, this is generally
noted on the 'Upload File' tool itself, in the FTP section paragraph.
This is the section for the public server:
The window on this tool is only appropriate for two types of upload
functions, either typing in text or entering a remote URL where data is
available. This remote URL could be to a FTP server, but the process is
different from loading local data (on your own computer) via FTP to the
The video (also linked from the wiki) for this tool demonstrates all
four methods for loading data. The first method is a basic browser
upload of a small file - which seems to be what you are asking about -
how can I help more with this part?
For deleting data, you can either delete individual datasets or complete
histories. Which are you having trouble with? There are two videos on
this wiki about datasets/histories, but it sounds like they are not
covering the part you need to know. If you want to provide more details,
I can try to help.
The server has been problematic this week, due to circumstances out of
our direct control, so if you had problems earlier, trying again is most
likely a good first pass solution. You can follow our Twitter feed for
updates about Main @galaxyproject - posted on our wiki here:
Usability matters, so helping you to get these operations working will
probably help others as well. And I can add into our documentation what
is unclear or missing. Plus most of our wiki is open - community members
are encouraged to add new pages or comments to fill in/share help ideas.
On 3/12/14 2:11 PM, Scott Tighe wrote:
> It is a total mystery how to get data uploaded. Just like it is a
> total mystery how to delete it. Spent an hour and a half reviewing
> your tutorials and trying FTP. The FTP does not work anymore and if
> you put the term usergalaxy.org in to the FTP window, it does not like
> that. The tutorials were not useful and appear to be based on FTP.
> Maybe you could do a tutorial on how exactly to upload like 10gB. Arrggg
> Scott Tighe
> Senior Core Laboratory Research Staff
> Advanced Genome Technologies Core
> NextGen Sequencing/Flow Cytometry
> University of Vermont and Vermont Cancer Center
> 149 Beaumont ave
> Health Science Research Facility 303/305
> Burlington Vermont 05405
> 802-656-2482 (AGTC)
> On 3/12/2014 1:17 PM, Jennifer Jackson wrote:
>> Hi Scott,
>> Is the 'Get Data -> Upload File' tool no longer functioning for you?
>> Can I help with using Main or is this on a local/cloud instance that
>> needs to be set up?
>> It is correct that the addition upload methods via the "Load Data"
>> process - found at the top of the tool panel - are not included in
>> our tutorials/vidoes yet. This is very new set of methods (first was
>> placed on Main at the end of January) and may still undergo some
>> changes. We expect this to stabilize near-term and then be
>> documented. Both tools will continue to co-exist.
>> If there are any usage question right now (you or others) please let
>> us know and we can help. The functions are either the same or very
>> similar to the 'Upload File' tool, just presented in a different
>> pop-up interface, plus now include convenience/feedback features.
>> Galaxy team
>> On 3/12/14 12:57 PM, Scott Tighe wrote:
>>> For all users:
>>> The tutorial on uploading data is incorrect. I do not think they
>>> have updated "how to upload data" yet.
>>> Scott Tighe
>>> Senior Core Laboratory Research Staff
>>> Advanced Genome Technologies Core
>>> NextGen Sequencing/Flow Cytometry
>>> University of Vermont and Vermont Cancer Center
>>> 149 Beaumont ave
>>> Health Science Research Facility 303/305
>>> Burlington Vermont 05405
>>> 802-656-2482 (AGTC)
>> Jennifer Hillman-Jackson
I deleted some files, because I reached 100% of the data volume I could use; my actual volume is 76 GB. I'm waiting now for an update from the server, that I reduced the data volume and can continue with my analysis. But I got a red note on the history for several times, that the update failed and that I should contact you, when it does so. What could I do now, to get an update from the server?
Thanks in advance!
I have a question about interpreting the cuffdiff data and how to pick up significant genes. I have genes which show ~8 fold change between 2 conditions: eg from FPKM of 0.08 to 28 and yet they are not significant. Is there is threshold of FPKM below which Cuffdiff does not consider it an FPKM to be valid and hence significance in "no"? What downstream analysis should I use to extract a meaningful list of genes from the Cuffdiff data?
Also, I filtered out FPKMs which were below 5 in both conditions? Is that reasonable?
I am trying to map sequences with Bowtie for Illumina. I have been waiting for a whole day now but it still says "Job is waiting to run". Are the jobs stuck in a queue or is there any other problem?
Thanks a lot in advance!
I am analysing some RNA-seq data and have two different datasets, total RNA plus enzyme and total RNA minus enzyme. I used to type in "column join" in the "Tools" menu on the Galaxy homepage after uploaded the files in Text delimited format. Column join allowed me to join two datasets by a hinge column, in this case I would choose column 1 which would be the chromosome position. I would also be allowed to fill empty columns with a value of 1. The output would give me 3 columns, chromosome number (which both datasets shared), reads for minus enzyme, and reads for plus enzyme. The function would never reject any chromosome position with reads in one dataset and not the other. However, I cannot seem to be able to find this function anymore, and the new function "Join two datasets" seems to only give me back rows where both plus and minus datasets have reads. Does anyone else have this problem or know how I could get around it?
Faculty of biological sciences
University of Leeds
I am PhD student and I am working with a bacterial transcriptome.
A few days ago, i have a problem to obtain data in DESeq and Edge-r on the
I get the message "no peek" at the end of the process, even with the task g
Have you had this problem?
I would like to find a solution...
Flavia Figueira Aburjaile
I have a tabular file and using compute (version 1.1.0) tool under text
manipulation menu, I 'm going to do a computation to find rows in which
column2 and 3 (c2 and c3) are similar in values (values are A,T,C and G) .
It seems the syntax for doing that is "c2==c3", but it dosent work. Can
Any help would be appreciated.